BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153374.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 37,877,850 number of mapped reads = 37,645,531 (99.39%) number of supplementary alignments = 225,811 (0.6%) number of secondary alignments = 0 number of mapped bases = 3,336,150,504 bp number of sequenced bases = 3,335,616,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,408,149 duplication rate = 44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.877 >>>>>>> ACTG content number of A's = 891,275,763 bp (26.72%) number of C's = 780,854,258 bp (23.41%) number of T's = 916,628,473 bp (27.48%) number of G's = 745,915,589 bp (22.36%) number of N's = 942,435 bp (0.03%) GC percentage = 45.77% >>>>>>> Mismatches and indels general error rate = 0.0023 number of mismatches = 7,337,308 number of insertions = 337,212 mapped reads with insertion percentage = 0.89% number of deletions = 265,326 mapped reads with deletion percentage = 0.7% homopolymer indels = 49.07% >>>>>>> Coverage mean coverageData = 1.0777X std coverageData = 13.12X There is a 12.35% of reference with a coverageData >= 1X There is a 8.33% of reference with a coverageData >= 2X There is a 3.65% of reference with a coverageData >= 3X There is a 2.93% of reference with a coverageData >= 4X There is a 2.13% of reference with a coverageData >= 5X There is a 1.9% of reference with a coverageData >= 6X There is a 1.68% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.46% of reference with a coverageData >= 9X There is a 1.39% of reference with a coverageData >= 10X There is a 1.32% of reference with a coverageData >= 11X There is a 1.26% of reference with a coverageData >= 12X There is a 1.21% of reference with a coverageData >= 13X There is a 1.17% of reference with a coverageData >= 14X There is a 1.12% of reference with a coverageData >= 15X There is a 1.08% of reference with a coverageData >= 16X There is a 1.05% of reference with a coverageData >= 17X There is a 1.01% of reference with a coverageData >= 18X There is a 0.98% of reference with a coverageData >= 19X There is a 0.95% of reference with a coverageData >= 20X There is a 0.93% of reference with a coverageData >= 21X There is a 0.9% of reference with a coverageData >= 22X There is a 0.87% of reference with a coverageData >= 23X There is a 0.85% of reference with a coverageData >= 24X There is a 0.83% of reference with a coverageData >= 25X There is a 0.81% of reference with a coverageData >= 26X There is a 0.79% of reference with a coverageData >= 27X There is a 0.77% of reference with a coverageData >= 28X There is a 0.75% of reference with a coverageData >= 29X There is a 0.73% of reference with a coverageData >= 30X There is a 0.71% of reference with a coverageData >= 31X There is a 0.7% of reference with a coverageData >= 32X There is a 0.68% of reference with a coverageData >= 33X There is a 0.66% of reference with a coverageData >= 34X There is a 0.65% of reference with a coverageData >= 35X There is a 0.64% of reference with a coverageData >= 36X There is a 0.62% of reference with a coverageData >= 37X There is a 0.61% of reference with a coverageData >= 38X There is a 0.6% of reference with a coverageData >= 39X There is a 0.58% of reference with a coverageData >= 40X There is a 0.57% of reference with a coverageData >= 41X There is a 0.56% of reference with a coverageData >= 42X There is a 0.55% of reference with a coverageData >= 43X There is a 0.54% of reference with a coverageData >= 44X There is a 0.53% of reference with a coverageData >= 45X There is a 0.52% of reference with a coverageData >= 46X There is a 0.51% of reference with a coverageData >= 47X There is a 0.5% of reference with a coverageData >= 48X There is a 0.49% of reference with a coverageData >= 49X There is a 0.48% of reference with a coverageData >= 50X There is a 0.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 349524722 1.4023023116159057 15.59347231943652 chr2 243199373 256596151 1.0550855778727686 11.647883698569094 chr3 198022430 184699430 0.932719742909932 10.524111331247273 chr4 191154276 135509924 0.7089034409044557 8.534245899825923 chr5 180915260 198547179 1.0974595454247476 12.095684379801444 chr6 171115067 114881995 0.6713727611140169 8.583496141280277 chr7 159138663 153593825 0.9651571912477359 11.451300688061933 chr8 146364022 214401318 1.4648498659048874 18.014626080021834 chr9 141213431 87950954 0.6228228673234347 7.941486405103751 chr10 135534747 168087803 1.2401823644530063 13.34734043437407 chr11 135006516 152126806 1.1268108422263114 11.549939584843948 chr12 133851895 172501494 1.2887489863329915 14.001450096223424 chr13 115169878 46541356 0.4041104914602757 6.222280943283665 chr14 107349540 96827152 0.9019801295841603 9.90915165726131 chr15 102531392 139234375 1.357968250348147 13.956629825676421 chr16 90354753 152917411 1.6924113665608715 26.793988182071494 chr17 81195210 123024429 1.515168554893817 13.358782223216764 chr18 78077248 38210493 0.4893934401991218 6.184599813745508 chr19 59128983 157027602 2.655679060131983 24.2419001373723 chr20 63025520 81449728 1.2923293294525773 14.019310693134898 chr21 48129895 34506670 0.71694879035161 9.100844571106434 chr22 51304566 42780879 0.8338610446485406 10.153907917525643 chrMT 16571 5877 0.3546557238549273 2.077298817362599 chrX 155270560 232465927 1.4971667971056457 16.862699000494324 chrY 59373566 2737004 0.046098022813721516 2.066523151981346